chr11-123725995-A-C

Variant names:

• chr11-123725995-A-C
• rs3183878
• NM_003455.4:c.*2T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003455.4(ZNF202):​c.*2T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 1,606,222 control chromosomes in the GnomAD database, including 122,328 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.41 (13035 hom., cov: 32)
  • Exomes 𝑓: 0.38 (109293 hom.)
• Consequence: ZNF202 NM_003455.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441
• Publications: 17 publications found

Genes affected

ZNF202 (HGNC:12994): (zinc finger protein 202) Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in chromosome; nuclear body; and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003455.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF202	NM_003455.4	MANE Select	c.*2T>G		3_prime_UTR	Exon 9 of 9	NP_003446.2
	ZNF202	NM_001301779.2		c.*2T>G		3_prime_UTR	Exon 8 of 8	NP_001288708.1
	ZNF202	NM_001301780.2		c.*2T>G		3_prime_UTR	Exon 7 of 7	NP_001288709.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF202	ENST00000530393.6	TSL:1 MANE Select	c.*2T>G		3_prime_UTR	Exon 9 of 9	ENSP00000432504.1
	ZNF202	ENST00000336139.8	TSL:1	c.*2T>G		3_prime_UTR	Exon 8 of 8	ENSP00000337724.4
	ZNF202	ENST00000529691.1	TSL:2	c.*2T>G		3_prime_UTR	Exon 7 of 7	ENSP00000433881.1

Frequencies

GnomAD3 genomes AF: 0.408 AC: 62005 AN: 151824 Hom.: 13035 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.415

GnomAD2 exomes AF: 0.365 AC: 89896 AN: 246386 AF XY: 0.365

Gnomad AFR exome AF: 0.489

Gnomad AMR exome AF: 0.317

Gnomad ASJ exome AF: 0.360

Gnomad EAS exome AF: 0.168

Gnomad FIN exome AF: 0.386

Gnomad NFE exome AF: 0.402

Gnomad OTH exome AF: 0.395

GnomAD4 exome AF: 0.384 AC: 558692 AN: 1454282 Hom.: 109293 Cov.: 48 AF XY: 0.382 AC XY: 276212 AN XY: 722512

African (AFR) AF: 0.505 AC: 16831 AN: 33344

American (AMR) AF: 0.323 AC: 14343 AN: 44428

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 9363 AN: 25534

East Asian (EAS) AF: 0.197 AC: 7817 AN: 39618

South Asian (SAS) AF: 0.318 AC: 27130 AN: 85260

European-Finnish (FIN) AF: 0.381 AC: 20199 AN: 52996

Middle Eastern (MID) AF: 0.489 AC: 2810 AN: 5746

European-Non Finnish (NFE) AF: 0.395 AC: 437189 AN: 1107240

Other (OTH) AF: 0.383 AC: 23010 AN: 60116

GnomAD4 genome AF: 0.408 AC: 62034 AN: 151940 Hom.: 13035 Cov.: 32 AF XY: 0.402 AC XY: 29838 AN XY: 74260

African (AFR) AF: 0.490 AC: 20309 AN: 41460

American (AMR) AF: 0.361 AC: 5513 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1287 AN: 3464

East Asian (EAS) AF: 0.176 AC: 905 AN: 5130

South Asian (SAS) AF: 0.311 AC: 1498 AN: 4816

European-Finnish (FIN) AF: 0.382 AC: 4030 AN: 10556

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27195 AN: 67918

Other (OTH) AF: 0.411 AC: 868 AN: 2114

Alfa AF: 0.408 Hom.: 19243

Bravo AF: 0.410

Asia WGS AF: 0.257 AC: 895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.91
DANN	Benign	0.74
PhyloP100		-0.44
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3183878; hg19: chr11-123596703;